Contacts of the helix formed by residues 228 - 243 (chain B) in PDB entry 1OKW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ARG* 3.4 47.9 + - - +
226B LYS 4.7 6.1 + - - -
227B LEU* 1.3 80.5 - - - +
229B ASN* 1.3 67.2 + - - +
230B GLU* 4.1 10.3 - - + +
231B THR* 3.2 21.2 + - - +
232B LEU* 3.6 4.5 + - - +
268B GLU* 5.0 9.2 - - + +
269B GLU* 2.7 24.2 + - - +
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Residues in contact with ASN 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 5.2 0.3 - - - +
227B LEU 4.6 3.6 - - - +
228B GLN* 1.3 76.3 + - - +
230B GLU* 1.3 62.7 + - - +
232B LEU* 3.1 12.9 - - - +
233B HIS* 3.1 26.2 + - - +
312B ASN* 4.1 15.3 - - - +
334B MET* 3.3 20.2 - - + +
338B GLU* 3.2 12.7 + - - +
412B LYS* 3.1 21.8 + - - -
413B TYR* 3.1 23.8 + - - -
418B TYR* 3.5 19.1 + - - -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL* 4.9 9.0 - - + -
228B GLN* 3.1 4.0 - - + +
229B ASN* 1.3 75.8 - - - +
231B THR* 1.3 57.5 + - - +
233B HIS* 3.0 3.7 + - - +
234B LEU* 2.7 45.6 + - + +
268B GLU* 3.4 37.0 - - + +
310B THR* 2.7 25.7 + - - +
312B ASN* 3.0 29.7 + - - +
313B GLN* 2.5 36.2 + - - +
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Residues in contact with THR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 4.3 9.2 - - + -
228B GLN* 3.2 11.0 + - - +
230B GLU* 1.3 77.8 - - - +
232B LEU* 1.3 54.6 + - - +
234B LEU* 3.3 8.0 + - - -
235B ALA* 2.8 32.7 + - - +
261B MET* 4.3 11.4 - - - -
264B ALA* 3.5 25.2 - - + +
265B SER* 3.7 21.5 - - - +
268B GLU* 3.7 16.7 - - - +
269B GLU* 2.9 23.7 + - - +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B VAL* 4.7 2.0 - - + -
218B LEU* 4.3 28.3 - - + +
219B VAL* 4.3 23.1 - - + -
222B GLY* 6.2 2.2 - - - -
228B GLN 3.6 3.9 + - - +
229B ASN* 3.1 14.7 + - - +
231B THR* 1.3 79.8 - - - +
233B HIS* 1.3 61.8 + - - +
235B ALA* 3.3 2.3 + - - +
236B VAL* 3.1 34.4 + - + +
261B MET* 4.5 14.2 - - + +
338B GLU* 4.0 26.5 - - + +
341B LEU* 3.3 26.0 - - + -
412B LYS* 4.6 5.2 - - - +
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Residues in contact with HIS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASN* 3.1 19.4 + - + +
230B GLU* 3.0 9.4 + - - +
232B LEU* 1.3 77.3 - - - +
234B LEU* 1.3 68.0 + - - +
236B VAL* 3.1 4.7 + - - +
237B ASN* 3.1 21.3 + - - +
310B THR* 3.7 22.6 - - + +
311B VAL* 3.9 32.0 - - + +
312B ASN* 4.0 23.1 + - + +
334B MET* 5.4 3.1 - - - -
337B GLY 4.2 7.0 + - - -
338B GLU* 3.8 30.1 - - + -
341B LEU* 3.5 36.7 - - + +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLU* 2.7 37.4 + - + +
231B THR* 3.5 4.5 - - - +
233B HIS* 1.3 75.2 - - - +
235B ALA* 1.3 62.5 + - - +
237B ASN* 3.3 3.8 + - - +
238B TYR* 3.1 36.1 + - - +
264B ALA* 3.9 11.2 - - + +
267B PHE* 3.8 28.5 - - + -
268B GLU* 3.9 24.5 - - + +
306B LEU 3.9 16.4 - - - +
307B ALA 5.1 0.4 - - - -
308B ALA* 3.5 31.0 - - + +
310B THR* 4.0 4.9 - - + -
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LEU* 4.6 8.7 - - + -
231B THR 2.8 19.2 + - - +
232B LEU 3.7 3.8 - - - +
233B HIS 3.2 0.4 - - - -
234B LEU* 1.3 72.0 - - - +
236B VAL* 1.3 62.9 + - - +
238B TYR* 3.1 10.6 + - - +
239B ILE* 3.0 26.7 + - - +
260B ALA* 3.8 6.0 - - + +
261B MET* 3.7 40.8 - - + +
264B ALA* 3.8 6.4 - - + +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG* 3.3 30.7 - - - +
215B VAL* 4.0 24.2 - - + -
218B LEU* 4.9 6.5 - - + -
232B LEU* 3.1 29.0 + - + +
233B HIS 3.1 6.3 + - - +
235B ALA* 1.3 75.1 - - - +
237B ASN* 1.3 65.9 + - - +
239B ILE* 3.3 9.7 + - + +
240B ASP* 2.9 27.0 + - - +
341B LEU* 4.0 24.9 - - + +
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Residues in contact with ASN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B CYS* 3.4 24.2 + - - +
195B PRO* 4.8 7.8 - - - +
233B HIS 3.1 12.6 + - - +
234B LEU* 3.3 11.2 - - - +
236B VAL* 1.3 77.6 - - - +
238B TYR* 1.3 65.1 + - + +
240B ASP* 3.3 4.8 + - - +
241B ARG* 2.5 61.8 + - - +
308B ALA* 3.4 21.4 - - + +
309B PRO 4.8 6.7 + - - +
310B THR* 5.6 2.7 - - + -
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Residues in contact with TYR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 3.1 35.9 + - + +
235B ALA* 3.1 6.0 + - - +
237B ASN* 1.3 89.0 - - - +
239B ILE* 1.3 58.5 + - - +
241B ARG* 3.4 5.1 + - - +
242B PHE* 2.8 32.7 + - - +
260B ALA* 4.0 25.6 - - + -
263B LEU* 4.3 10.1 - - + -
264B ALA* 3.8 24.5 - - + -
267B PHE* 4.2 6.6 - - - +
298B VAL* 4.8 3.8 - - + -
302B LEU* 3.8 29.0 - - + +
306B LEU* 2.7 58.7 + - + +
308B ALA* 4.7 0.4 - - + -
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG* 5.4 5.8 - - + +
214B LEU* 3.9 18.6 - - + -
215B VAL* 5.5 4.5 - - + -
218B LEU* 3.6 30.1 - - + -
235B ALA 3.0 15.1 + - - +
236B VAL* 3.5 12.3 - - + +
238B TYR* 1.3 77.2 - - - +
240B ASP* 1.3 66.7 + - - +
242B PHE* 3.2 5.5 + - - +
243B LEU* 2.8 51.2 + - + +
256B VAL* 4.5 10.5 - - + +
257B GLY* 3.7 20.2 - - - -
260B ALA* 3.7 15.0 - - + -
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B PRO* 3.8 23.4 - - + +
199B TYR* 2.6 38.3 + - + -
211B ARG* 2.8 37.3 + - - -
236B VAL* 2.9 21.5 + - - +
237B ASN* 4.0 1.9 - - - +
239B ILE* 1.3 82.1 - - - +
241B ARG* 1.3 52.6 - - - +
243B LEU 3.6 1.7 + - - -
244B SER* 2.2 34.2 + - - -
348B LEU* 3.9 12.3 - - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B CYS* 3.6 37.0 + - - +
194B LYS 4.6 3.1 - - - +
195B PRO* 4.3 14.8 - - + -
237B ASN* 2.5 52.5 + - - +
238B TYR* 3.8 12.7 - - - -
240B ASP* 1.3 76.2 - - - +
242B PHE* 1.3 64.0 + - - +
244B SER* 3.1 20.7 + - - -
245B SER* 3.6 9.0 + - - -
301B VAL* 5.0 0.5 - - - +
302B LEU* 3.8 35.1 + - + +
305B ASP* 2.8 42.8 + - - +
308B ALA* 4.0 9.5 - - - +
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Residues in contact with PHE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B TYR 2.8 20.3 + - - +
239B ILE* 3.4 5.8 - - - +
241B ARG* 1.3 71.8 - - - +
243B LEU* 1.3 67.1 + - + +
244B SER 2.8 10.4 + - - -
245B SER* 3.0 12.1 + - - -
246B MET* 3.1 34.8 + - + +
248B VAL* 4.1 7.0 - - + -
256B VAL* 3.8 33.7 - - + -
294B MET* 4.2 15.9 - - - -
297B LEU* 4.0 7.6 - - + -
298B VAL* 3.8 34.3 - - + -
301B VAL* 3.7 38.1 - - + -
302B LEU* 4.2 4.3 - - + +
26C THR* 4.2 10.8 - - + -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B TYR* 3.2 43.3 - - + +
200B MET* 4.6 3.4 - - + -
203B GLN* 2.7 30.6 + - - +
206B ILE* 3.8 20.6 - - + -
211B ARG* 5.5 3.6 - - + -
239B ILE* 2.8 36.4 + - + +
241B ARG 3.4 0.2 - - - -
242B PHE* 1.3 79.0 - - + +
244B SER* 1.3 58.6 + - - +
245B SER 3.4 0.4 - - - -
246B MET 4.0 1.6 + - - +
248B VAL* 3.4 37.0 - - + -
253B LEU* 3.8 17.5 - - + -
256B VAL* 4.8 3.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il